Hi João, Before diving into the hassle of installing additional compilers (which probably won't make a difference) I recommend to get familiar with a debugger like gdb and obtain a stack trace of the crash.
To compile PyMOL with debug symbols, do export DEBUG=1 before running setup.py. Then run PyMOL (actually: python) with gdb. There is a bit of a learning curve to get familiar with gdb, but considering that you already spend time on this problem and are willing to spend more, I think it's worthwhile. Cheers, Thomas On 11 Apr 2017, at 19:08, João M. Damas <jmda...@itqb.unl.pt> wrote: > Thanks for the feedback, Folmer! > > I am using CentOS. I already used --use-msgpackc=no and it did not improve. > gcc --version gives me 4.8.5 (I cannot update more). Do you think it would be > worth it to install gcc 4.9? On the install page there was said that a > regression to 4.4 could work, but I don’t know. > > Anyone else using CentOS having problems with pymol installation? > > Thanks, > João > > > On Wed, Mar 29, 2017 at 10:35 AM, Folmer Fredslund <folm...@gmail.com> wrote: > Hi João, > > On Ubuntu 16.04 (you didn't mention what you were running) with gcc-4.9 and > "--use-msgpackc=no" I get a working pymol with revision 4170. > > Have you tried creating a new user and test pymol from that account? That > should help you identify if it is solely a problem with your own account. > > HTH, > Folmer > > > On 2017-03-28 03:15, João M. Damas wrote: >> Nobody experiencing the same issues? Any tips on what I may be doing wrong >> on the installation? >> >> João >> >> On Fri, Mar 17, 2017 at 4:08 PM, João M. Damas <jmda...@itqb.unl.pt> wrote: >> Dear all, >> >> I started experiencing segmentation fault on a pymol that I had installed >> through the omnia channel on conda. >> >> Then, I decided to install from scratch using this recipe: >> https://pymolwiki.org/index.php/Linux_Install#Get_latest_source_from_SVN >> >> Still getting the segmentation fault, so maybe something changed in my >> system and it's conflicting with? >> >> The segmentation fault is not on launching PyMOL, but rather when I do >> stuff: loading a PDB file, building a fragment. Like this: >> >> ``` >> ./pymol: line 3: 28505 Segmentation fault "/usr/bin/python2.7" >> "/data/joao/maindisk/software/pymol-svn/modules/pymol/__init__.py" "$@" >> ``` >> >> Curiously, when I load a 1.740 session (.pse file I had saved), it works (no >> segmentation fault), I can even perform commands like select and stuff, and >> they work. If I load a more recent 1.803 session, it also seg faults: >> >> ``` >> Executive: Loading version 1.803 session... >> ./pymol: line 3: 29221 Segmentation fault "/usr/bin/python2.7" >> "/data/joao/maindisk/software/pymol-svn/modules/pymol/__init__.py" "$@" >> ``` >> >> Any clues? Am I doing something wrong? >> >> Thanks, >> João >> >> -- >> João M. Damas >> PhD Student >> Protein Modelling Group >> ITQB-UNL, Oeiras, Portugal >> Tel:+351-214469613 -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
